diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index 310aeb34b3708afe1a4db6332bee07748f654690..cad4927a7a694765bd394dee1eeaa65c57182f39 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -4410,19 +4410,23 @@ rule make_gene_list_lfc_boxplots: lfc_data = pd.read_table(input.data, index_col="gene") for (list_name, id_list) in params.id_lists.items(): try: - selected_rows = lfc_data.loc[lfc_data.index.intersection(id_list)] + selected_rows = lfc_data.loc[lfc_data.index.intersection(id_list)] except TypeError as err: print(params.id_lists) print(type(id_list)) print(lfc_data.index.intersection(id_list)) raise - selected_data = selected_rows[wildcards.fold_type] + if wildcards.fold_type in RPM_FOLD_TYPES: + fold_type = "mean_log2_RPM_fold" + else: + fold_type = wildcards.fold_type + selected_data = selected_rows[fold_type] lfcs_dict[list_name] = selected_data lfcs = pd.DataFrame(lfcs_dict) # lfcs = pd.DataFrame( # {list_name : lfc_data.loc[set(id_list)][wildcards.fold_type] for ( # list_name, id_list) in params.id_lists.items()}) - title = f"{wildcards.small_type} folds for {wildcards.contrast}" + title = f"{wildcards.small_type} {wildcards.fold_type} for {wildcards.contrast}" try: save_plot( output.boxplots, @@ -4484,7 +4488,7 @@ rule make_contrast_lfc_boxplots: # set(id_list)]["mean_log2_RPM_fold"] for ( # contrast, filename) in zip(contrasts_dict["ip"], input.data) for ( # list_name, id_list) in params.id_lists.items()}) - title=f"{wildcards.small_type} folds for {wildcards.contrast_type} contrasts" + title=f"{wildcards.small_type} {wildcards.fold_type} for {wildcards.contrast_type} contrasts" try: save_plot( output.boxplots, @@ -4505,7 +4509,6 @@ rule make_contrast_lfc_boxplots: raise - rule make_biotype_lfc_boxplots: """For a given gene list, make one box for each contrast.""" input: